Contacts of the helix formed by residues 662 - 678 (chain Z) in PDB entry 5WTI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 662 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661Z ASP* 1.3 77.9 - - + +
663Z THR* 1.3 63.6 + - - +
665Z ARG* 4.0 6.2 - - - +
666Z GLU* 3.4 22.7 + - - +
697Z TYR* 6.1 5.0 - - - +
698Z LYS 5.6 6.3 - - - +
703Z TRP* 6.0 1.6 - - - -
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Residues in contact with THR 663 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661Z ASP 3.3 4.9 - - - +
662Z ILE* 1.3 79.7 - - - +
664Z GLU* 1.3 62.3 + - - +
666Z GLU* 3.8 2.5 + - - +
667Z LYS* 3.3 21.4 + - - +
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Residues in contact with GLU 664 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661Z ASP* 3.8 8.9 + - - +
663Z THR* 1.3 77.2 - - - +
665Z ARG* 1.3 61.1 + - - +
667Z LYS* 3.5 7.6 - - - +
668Z ARG* 2.8 33.4 + - + +
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Residues in contact with ARG 665 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656Z PHE* 5.8 1.2 - - - -
658Z GLN 4.3 8.3 - - - +
661Z ASP 3.2 20.2 + - - +
662Z ILE* 4.2 5.6 - - - +
663Z THR 3.4 0.4 - - - -
664Z GLU* 1.3 77.1 - - - +
666Z GLU* 1.3 61.0 + - - +
668Z ARG* 4.2 3.3 - - - +
669Z VAL* 3.2 25.8 + - - +
696Z MET 5.1 2.2 - - - +
703Z TRP* 3.4 39.2 - - + -
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Residues in contact with GLU 666 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662Z ILE 3.4 15.7 + - - +
663Z THR 4.3 2.7 - - - +
664Z GLU 3.3 0.2 - - - -
665Z ARG* 1.3 78.3 - - - +
667Z LYS* 1.3 60.5 + - - +
669Z VAL* 4.2 5.9 - - - +
670Z THR* 3.4 21.3 + - - -
696Z MET* 3.8 27.7 + - + +
697Z TYR* 5.5 3.4 - - + -
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Residues in contact with LYS 667 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663Z THR 3.3 17.8 + - - +
664Z GLU* 3.0 10.4 + - - +
666Z GLU* 1.3 77.2 - - - +
668Z ARG* 1.3 63.7 + - - +
670Z THR* 3.4 6.7 + - - -
671Z LYS* 3.2 19.6 + - - +
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Residues in contact with ARG 668 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655Z HIS* 6.0 1.8 - - - +
656Z PHE* 4.2 20.6 - - + -
664Z GLU 2.8 19.2 + - - +
665Z ARG* 4.3 3.8 - - - +
667Z LYS* 1.3 69.6 - - - +
669Z VAL* 1.3 62.4 + - - +
671Z LYS* 2.9 23.8 + - - +
672Z TRP* 3.1 13.7 + - - +
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Residues in contact with VAL 669 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656Z PHE* 4.4 23.2 - - + -
665Z ARG 3.2 18.1 + - - +
666Z GLU* 4.5 4.3 - - - +
668Z ARG* 1.3 77.4 - - - +
670Z THR* 1.3 60.0 + - - +
672Z TRP* 3.7 2.3 + - - +
673Z ILE* 3.4 22.5 + - - +
696Z MET* 5.4 11.0 - - + -
703Z TRP* 6.2 3.4 - - + -
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Residues in contact with THR 670 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666Z GLU 3.4 18.1 + - - -
667Z LYS* 3.4 8.4 + - - -
668Z ARG 3.1 0.8 - - - -
669Z VAL* 1.3 77.6 - - - +
671Z LYS* 1.3 61.3 + - - +
673Z ILE* 4.0 6.5 - - - +
674Z SER* 3.3 22.7 + - - -
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Residues in contact with LYS 671 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667Z LYS 3.2 11.7 + - - +
668Z ARG* 2.9 14.6 + - - +
670Z THR* 1.3 77.2 - - - +
672Z TRP* 1.3 63.6 + - - +
674Z SER* 3.6 4.3 + - - -
675Z ARG* 3.3 22.5 + - - +
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Residues in contact with TRP 672 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652Z ASN* 4.2 14.6 - - - +
656Z PHE* 3.8 30.7 - - + -
668Z ARG 3.1 6.1 + - - +
669Z VAL 4.3 2.9 - - - +
670Z THR 3.5 0.2 - - - -
671Z LYS* 1.3 74.8 - - - +
673Z ILE* 1.3 63.0 + - - +
674Z SER 3.4 0.2 - - - -
675Z ARG* 3.8 6.4 + - - +
676Z GLN* 3.4 20.1 + - - +
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Residues in contact with ILE 673 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669Z VAL 3.4 16.4 + - - +
670Z THR* 4.2 5.8 - - - +
671Z LYS 3.3 0.6 - - - -
672Z TRP* 1.3 77.4 - - - +
674Z SER* 1.3 63.0 + - - +
676Z GLN* 3.3 15.0 + - - +
677Z GLU* 3.4 12.1 + - - +
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Residues in contact with SER 674 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670Z THR 3.3 16.3 + - - -
671Z LYS* 4.0 5.8 - - - -
672Z TRP 3.4 0.2 - - - -
673Z ILE* 1.3 80.8 - - - +
675Z ARG* 1.3 59.5 - - - +
676Z GLN 3.5 0.2 + - - -
677Z GLU* 3.5 7.8 + - - +
678Z ASN* 3.4 18.5 + - - +
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Residues in contact with ARG 675 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671Z LYS 3.3 14.4 + - - +
672Z TRP* 4.2 7.2 - - - +
673Z ILE 3.3 0.2 - - - -
674Z SER* 1.3 77.0 - - - +
676Z GLN* 1.3 62.8 + - - +
678Z ASN* 3.4 21.8 + - + +
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Residues in contact with GLN 676 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672Z TRP 3.4 12.8 + - - +
673Z ILE* 3.3 12.9 + - - +
674Z SER 3.2 0.8 - - - -
675Z ARG* 1.3 78.9 - - - +
677Z GLU* 1.3 60.7 + - - +
678Z ASN 3.5 2.8 + - - -
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Residues in contact with GLU 677 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673Z ILE 3.4 9.4 + - - +
674Z SER* 4.0 8.7 - - - +
675Z ARG 3.4 0.4 - - - -
676Z GLN* 1.3 76.5 - - - +
678Z ASN* 1.3 63.7 + - - +
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Residues in contact with ASN 678 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674Z SER 3.4 11.1 + - - +
675Z ARG* 3.5 21.1 - - + +
676Z GLN 3.2 4.3 - - - -
677Z GLU* 1.3 83.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il